We report on structural characterization of void-structures created by a micro-explosion at the locus of a tightly focused femtosecond laser pulse inside the crystalline phase of Al2O3 (R3c space group). The transmission electron microscopy (TEM), micro-X-ray diffraction (XRD) analysis, and Raman scattering revealed a presence of strongly structurally modified amorphous regions around the void-structures. We discuss issues of achieving the required resolution for structural characterization and assignment of newly formed phases of nano-crystallites by TEM, XRD, and Raman scattering from micro-volumes of modified materials enclosed inside the bulk of the host phase.